Fungal assist microalgal cultivation is getting substantial considerations due to the highly efficiency of bioflocculation process without requirements of added chemicals and little bit energy input. So, Fungi pelletization-assisted microalgal cultivation were applied for improving algal harvesting process and nutrient recovery as step wise for wastewater treatment. Two strains of microalgae (Nannochloropsis salina and Chlorella salina) and three species of fungi (Penicillium chrysogenum, Aspergillus niger and Aspergillus fumigatus) were used to evaluate the effect of fungi–algae pelletization process on wastewater recovery. After 48 hour of cultivation, the highest flocculation efficiency (98.9%) was recorded by A. fumigatus assist C. salina, while the lowest percentage (85.9%) recorded by A. niger assist N. Salina. The highest nutrient removal percentage was for nitrite by A. niger assist C. salina /tap water (98.4%) followed by phosphate A. fumigates assist N. salina/sea and tap water (90.9%), then ammonia by A. fumigates assist N. salina /seawater (89.5%).. This study concluded that the bioflocculation technique is a highly promising compared to traditional algal harvesting techniques and other biological wastewater treatment methods.